Markers + reference

Heliotropium

3 species · Heliotropiaceae · Boraginales

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Species 3
Genome length 155–156 kb
Candidate markers 271
Primer pairs 95

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 305 0.0759 0.92 75.9 yes View details
rps16-trnQ-UUG LSC 635 0.0386 0.99 74.2 yes View details
trnS-GCU-trnG-GCC LSC 745 0.0385 1.00 73.4 yes View details
psbM-trnD-GUC LSC 942 0.0287 1.00 71.1 yes View details
ndhC-trnV-UAC LSC 1048 0.0382 1.00 74.9 yes View details
ycf1 IRb 1188 0.0171 1.00 57.1 no View details
ndhF SSC 2268 0.0231 0.99 58.5 yes View details
ndhF-rpl32 SSC 793 0.0368 0.99 72.8 yes View details
rpl32-trnL-UAG SSC 717 0.0490 0.98 85.4 yes View details
ycf1 SSC 5502 0.0255 1.00 55.0 yes View details
trnL-UAG-ccsA SSC 114 0.0731 1.00 82.0 yes View details
trnW-CCA-trnP-UGG LSC 161 0.0414 1.00 77.9 yes View details
petD-rpoA LSC 194 0.0533 1.00 75.4 yes View details
rpl16-rps3 LSC 122 0.0519 1.00 74.9 yes View details
rpl2-trnH-GUG IRa 111 0.0472 0.95 74.7 no View details
trnS-GGA-rps4 LSC 276 0.0326 1.00 73.2 yes View details
ndhD-psaC SSC 93 0.0580 0.99 72.9 yes View details
psaA-ycf3 LSC 675 0.0188 1.00 72.4 yes View details
trnC-GCA-petN LSC 787 0.0246 0.98 71.9 yes View details
trnG-GCC-trnfM-CAU LSC 175 0.0400 1.00 71.2 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA ATATTATGGGCGAACGACGG GTTGATAGTCAAGGCCGTGT 531 0.333 52.0
trnH-GUG-psbA_p2 trnH-GUG-psbA ATATTATGGGCGAACGACGG GGCTGAGCACAACATCCTTA 889 0.333 51.8
trnH-GUG-psbA_p3 trnH-GUG-psbA ATATTATGGGCGAACGACGG GTATTCCAGGCTGAGCACAA 897 0.333 51.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ATATTATGGGCGAACGACGG TATTCCAGGCTGAGCACAAC 896 0.333 51.8
trnH-GUG-psbA_p5 trnH-GUG-psbA ATATTATGGGCGAACGACGG TTGTATTCCAGGCTGAGCAC 899 0.333 51.8
trnK-UUU_p1 trnK-UUU ACTCCCAAGCACACGAATTT CCACAGGCTTGGTTTTGACT 2989 0.333 48.4
trnK-UUU_p2 trnK-UUU GACTCCCAAGCACACGAATT CCACAGGCTTGGTTTTGACT 2990 0.333 44.7
trnK-UUU_p3 trnK-UUU ACTCCCAAGCACACGAATTT CCTTTTGTCCCACAGGCTT 2998 0.333 44.1
trnK-UUU_p4 trnK-UUU CCCAAGCACACGAATTTTCT TTGTCCCTTTTGTCCCACAG 3000 0.333 44.1
trnK-UUU_p5 trnK-UUU ACTCCCAAGCACACGAATTT GTCCCACAGGCTTGGTTTT 2992 0.333 43.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTC GCTATTCGGAGGTTCGAGTC 704–1120 1.000 83.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTC TATTCGGAGGTTCGAGTCCT 702–1118 1.000 80.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTC ATTCGGAGGTTCGAGTCCTT 701–1117 1.000 80.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GCTATTCGGAGGTTCGAGTC 731–1147 1.000 80.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GCTATTCGGAGGTTCGAGTC 730–1146 1.000 80.1
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 819–887 1.000 56.6
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CTTTAGTCCACTCAGCCACC ACGAATCACACTTTTACCACT 804–872 1.000 56.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 868–936 1.000 55.4
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CCATCAACGGAAAGAGAGGG ACGAATCACACTTTTACCACT 874 0.333 24.8
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CCATCAACGGAAAGAGAGGG AACGAATCACACTTTTACCACT 875 0.333 22.9
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 897–988 1.000 84.9
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTCTTCCCCACACTACGAGT 895–986 1.000 84.9
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 898–989 1.000 84.3
trnC-GCA-petN_p4 trnC-GCA-petN GTATCATTTTGGCGGCATGG TTCTTCCCCACACTACGAGT 947–1038 1.000 84.2
trnC-GCA-petN_p5 trnC-GCA-petN GTATCATTTTGGCGGCATGG ACTTCTTCCCCACACTACGA 949–1040 1.000 84.1
psbM-trnD-GUC_p1 psbM-trnD-GUC AGTAGAAAAGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 1074–1267 1.000 58.9
psbM-trnD-GUC_p2 psbM-trnD-GUC AGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 1066–1259 1.000 58.8
psbM-trnD-GUC_p3 psbM-trnD-GUC AAGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 1067–1260 1.000 57.2
psbM-trnD-GUC_p4 psbM-trnD-GUC AGCGGTAGGAACTAGAATGAA TTCAATTGGTCAGAGCACCG 1066–1259 1.000 57.2
psbM-trnD-GUC_p5 psbM-trnD-GUC AAGTAGAAAAGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 1075–1268 1.000 56.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Heliotropium arbainense NC_084200.1 154709 View on NCBI ↗
Heliotropium arborescens NC_066966.1 156243 View on NCBI ↗
Heliotropium foertherianum NC_073098.1 155865 View on NCBI ↗